Scott -- The attached file was the output of the antechamber bondtype
program. Curiously, in Amber16, all the bond types in the output file were
only single or double bonds. It might be the case that bond types in the
input file (bfd_atoms.ac) to bondtype are getting propagated to the output
file? The bondtypes in the input file come from our own atom/bond typing
software which was developed 3-4 years ago to support atom types for our
solvation model. Our bond typer handles certain, rare chemical structures
better than the antechamber bondtype program. This is based on running
both programs on our fragment database of ~4,000 fragments. I'm hoping to
run both ours and antechamber on the whole zinc database sometime soon for
further comparison. As you probably know, bond type assignments using just
valence constraints are occasionally ambiguous, but can be further resolved
by rules of thumb (neutral preferred over charged) or ultimately QM.
-- John
On Wed, Aug 15, 2018 at 1:48 PM Scott Brozell <sbrozell.rci.rutgers.edu>
wrote:
> Hi,
>
> On Wed, Aug 08, 2018 at 02:56:04PM -0400, David A Case wrote:
> > On Wed, Aug 08, 2018, John L. Kulp, Jr. wrote:
> >
> > > In AmberTools18, checkmolecule.c check_input_molecule() part 4 bond
> check,
> > > the valence calculation does not check for bond types 7 and 8 and thus
> > > fails. See attached fix which works for me.
> >
> > Thanks for the report...looks like a straightforward change. Do you
> > have an example of where the current code fails (so that we can test,
> > and add a regression test?) I'm assuming Scott Brozell will be
> > following this thread as well, and may have additional comments or
> > questions.
>
> Yes, thanks for the report, but after glancing at the code,
> i wonder how you got such bond types ? So an example is important.
>
> thanks,
> scott
>
>
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Received on Thu Aug 16 2018 - 06:00:02 PDT
